How can I explicitly free memory in Python

Question

I wrote a Python program that acts on a large input file to create a few million objects representing triangles   The algorithm is    read an input file process the file and create a list of triangles  represented by their vertices output the vertices in the OFF format  a list of vertices followed by a list of triangles   The triangles are represented by indices into the list of vertices   The requirement of OFF that I print out the complete list of vertices before I print out the triangles means that I have to hold the list of triangles in memory before I write the output to file   In the meanwhile I m getting memory errors because of the sizes of the lists     What is the best way to tell Python that I no longer need some of the data  and it can be freed

User · Answer

Unfortunately  depending on your version and release of Python  some types of objects use  free lists  which are a neat local optimization but may cause memory fragmentation  specifically by making more and more memory  earmarked  for only objects of a certain type and thereby unavailable to the  general fund    The only really reliable way to ensure that a large but temporary use of memory DOES return all resources to the system when it s done  is to have that use happen in a subprocess  which does the memory-hungry work then terminates  Under such conditions  the operating system WILL do its job  and gladly recycle all the resources the subprocess may have gobbled up  Fortunately  the multiprocessing module makes this kind of operation  which used to be rather a pain  not too bad in modern versions of Python   In your use case  it seems that the best way for the subprocesses to accumulate some results and yet ensure those results are available to the main process is to use semi-temporary files  by semi-temporary I mean  NOT the kind of files that automatically go away when closed  just ordinary files that you explicitly delete when you re all done with them

User · Answer

Python is garbage-collected  so if you reduce the size of your list  it will reclaim memory   You can also use the  del  statement to get rid of a variable completely   biglist    blah blah blah       del biglist

User · Answer

As other answers already say  Python can keep from releasing memory to the OS even if it s no longer in use by Python code  so gc collect   doesn t free anything  especially in a long-running program  Anyway if you re on Linux you can try to release memory by invoking directly the libc function malloc trim  man page   Something like  import ctypes libc   ctypes CDLL  quot libc so 6 quot   libc malloc trim 0

User · Answer

According to Python Official Documentation  you can force the Garbage Collector to release unreferenced memory with gc collect    Example   import gc gc collect

User · Answer

If you don t care about vertex reuse  you could have two output files--one for vertices and one for triangles  Then append the triangle file to the vertex file when you are done

User · Answer

I had a similar problem in reading a graph from a file  The processing included the computation of a 200 000x200 000 float matrix  one line at a time  that did not fit into memory  Trying to free the memory between computations using gc collect   fixed the memory-related aspect of the problem but it resulted in performance issues  I don t know why but even though the amount of used memory remained constant  each new call to gc collect   took some more time than the previous one  So quite quickly the garbage collecting took most of the computation time   To fix both the memory and performance issues I switched to the use of a multithreading trick I read once somewhere  I m sorry  I cannot find the related post anymore   Before I was reading each line of the file in a big for loop  processing it  and running gc collect   every once and a while to free memory space  Now I call a function that reads and processes a chunk of the file in a new thread  Once the thread ends  the memory is automatically freed without the strange performance issue   Practically it works like this   from dask import delayed    this module wraps the multithreading def f storage  index  chunk size      the processing function       read the chunk of size chunk size starting at index in the file       process it using data in storage if needed       append data needed for further computations  to storage      return storage  partial result   delayed        put into the delayed   the constructor for your data structure   I personally use  delayed nx Graph     since I am creating a networkx Graph chunk size   100    ideally you want this as big as possible while still enabling the computations to fit in memory for index in range 0  len file   chunk size         we indicates to dask that we will want to apply f to the parameters partial result  index  chunk size     partial result   delayed f  partial result  index  chunk size         no computations are done yet         dask will spawn a thread to run f partial result  index  chunk size  once we call partial result compute         passing the previous  partial result  variable in the parameters assures a chunk will only be processed after the previous one is done       it also allows you to use the results of the processing of the previous chunks in the file if needed    this launches all the computations result   partial result compute      one thread is spawned for each  delayed  one at a time to compute its result   dask then closes the tread  which solves the memory freeing issue   the strange performance issue with gc collect   is also avoided

User · Answer

Others have posted some ways that you might be able to  coax  the Python interpreter into freeing the memory  or otherwise avoid having memory problems    Chances are you should try their ideas out first   However  I feel it important to give you a direct answer to your question     There isn t really any way to directly tell Python to free memory   The fact of that matter is that if you want that low a level of control  you re going to have to write an extension in C or C     That said  there are some tools to help with this    cython swig boost python

User · Answer

The del statement might be of use  but IIRC it isn t guaranteed to free the memory  The docs are here     and a why it isn t released is here     I have heard people on Linux and Unix-type systems forking a python process to do some work  getting results and then killing it    This article has notes on the Python garbage collector  but I think lack of memory control is the downside to managed memory

User · Answer

You can t explicitly free memory  What you need to do is to make sure you don t keep references to objects  They will then be garbage collected  freeing the memory   In your case  when you need large lists  you typically need to reorganize the code  typically using generators iterators instead  That way you don t need to have the large lists in memory at all   http   www prasannatech net 2009 07 introduction-python-generators html

User · Answer

del can be your friend  as it marks objects as being deletable when there no other references to them  Now  often the CPython interpreter keeps this memory for later use  so your operating system might not see the  freed  memory    Maybe you would not run into any memory problem in the first place by using a more compact structure for your data  Thus  lists of numbers are much less memory-efficient than the format used by the standard array module or the third-party numpy module   You would save memory by putting your vertices in a NumPy 3xN array and your triangles in an N-element array

[python] How can I explicitly free memory in Python?

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